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Publications Citing NeuroMorphoVis

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marwan-abdellah edited this page Aug 19, 2024 · 13 revisions

Publications Using or Mentioning NeuroMorphoVis

* This list is last updated on August 2024.

2024

  • Reimer, Marike L., Sierra D. Kauer, Curtis A. Benson, Jared F. King, Siraj Patwa, Sarah Feng, Maile A. Estacion, Lakshmi Bangalore, Stephen G. Waxman, and Andrew M. Tan. "A FAIR, open-source virtual reality platform for dendritic spine analysis." Patterns (2024). doi:10.1016/j.patter.2024.101041

  • Zehtabian, Amin, Joachim Fuchs, Britta J. Eickholt, and Helge Ewers. "Automated Analysis of Neuronal Morphology in 2D Fluorescence Micrographs through an Unsupervised Semantic Segmentation of Neurons." Neuroscience (2024). doi:10.1016/j.neuroscience.2024.05.024

  • Leite, Jéssica, Fabiano Nhoatto, Antonio Jacob Jr, Roberto Santana, and Fábio Lobato. "Computational Tools for Neuronal Morphometric Analysis: A Systematic Search and Review." Neuroinformatics (2024): 1-25. doi:10.1007/s12021-024-09674-6

  • Habbal, Osama, Ahmad Farhat, Reem Khalil, and Christopher Pannier. "Application of fused filament fabrication 3D printing and molding to produce flexible, scaled neuron morphology models." Rapid Prototyping Journal 30, no. 11 (2024): 192-204. doi:10.1108/RPJ-10-2023-0378

  • Velasco, Ivan, Juan J. Garcia-Cantero, Juan P. Brito, Sofia Bayona, Luis Pastor, and Susana Mata. "NeuroEditor: a tool to edit and visualize neuronal morphologies." Frontiers in Neuroanatomy 18 (2024): 1342762. doi:10.3389/fnana.2024.1342762

  • Groden, Moritz, Hannah M. Moessinger, Barbara Schaffran, Javier DeFelipe, Ruth Benavides-Piccione, Hermann Cuntz, and Peter Jedlicka. "A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites." PLOS Computational Biology 20, no. 2 (2024): e1011267. doi:10.1371/journal.pcbi.1011267

  • Abdellah, Marwan, Alessandro Foni, Juan José García Cantero, Nadir Román Guerrero, Elvis Boci, Adrien Fleury, Jay S. Coggan et al. "Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling." bioRxiv (2024): 2024-03.

  • Chen, Jie, and Lonxin Le. "Neuronal visualization with Bézier curves SDF rendering and accelerated volume rendering." In International Conference on Image, Signal Processing, and Pattern Recognition (ISPP 2024), vol. 13180, pp. 1796-1801. SPIE, 2024. Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling doi:10.1117/12.3034069

2023

  • Jiang, Jiaxiang, Michael Goebel, Cezar Borba, William Smith, and B. S. Manjunath. "3D Neuron Morphology Analysis." Research Square (2023). doi:10.21203/rs.3.rs-2698751/v1

  • Jiang, Jiaxiang, Michael Goebel, Cezar Borba, William Smith, and B. S. Manjunath. "A robust approach to 3D neuron shape representation for quantification and classification." BMC bioinformatics 24, no. 1 (2023): 366. doi:10.1186/s12859-023-05482-y

  • Ecker, András, Daniela Egas Santander, Marwan Abdellah, Jorge Blanco Alonso, Sirio Bolaños-Puchet, Giuseppe Chindemi, Dhuruva Priyan Gowri Mariyappan et al. "Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome." bioRxiv (2023): 2023-08. doi:10.1101/2023.08.07.552264

  • Isbister, James B., András Ecker, Christoph Pokorny, Sirio Bolaños-Puchet, Daniela Egas Santander, Alexis Arnaudon, Omar Awile et al. "Modeling and simulation of neocortical micro-and mesocircuitry. Part II: Physiology and experimentation." bioRxiv (2023): 2023-05. doi:10.1101/2023.05.17.541168

  • Leite, Jéssica, Fabiano Nhoatto, Antonio Jacob Jr, Roberto Santana, and Fábio Lobato. "Computational Tools for Neuronal Morphometric Analysis: A Systematic Search and Review." Neuroinformatics (2024): 1-25. doi:10.1007/s12021-024-09674-6

  • Romani, Armando, Alberto Antonietti, Davide Bella, Julian Budd, Elisabetta Giacalone, Kerem Kurban, Sára Sáray et al. "Community-based Reconstruction and Simulation of a Full-scale Model of Region CA1 of Rat Hippocampus." bioRxiv (2023): 2023-05. [doi:10.1101/2023.05.17.541167](doi: https://doi.org/10.1101/2023.05.17.541167 )

  • Iavarone, Elisabetta, Jane Simko, Ying Shi, Marine Bertschy, María García-Amado, Polina Litvak, Anna-Kristin Kaufmann et al. "Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep." Cell Reports 42, no. 3 (2023). doi:10.1016/j.celrep.2023.112200

  • Velasco González, Iván. "Técnicas de visualización interactiva para la exploración y análisis de datos complejos. Aplicación en el ámbito médico." (2023).

  • Keto, Laura, and Tiina Manninen. "CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations." Neuroinformatics (2023): 1-18. doi:10.1007/s12021-023-09627-5

  • Abdellah, Marwan, Juan José García Cantero, Nadir Román Guerrero, Alessandro Foni, Jay S. Coggan, Corrado Calì, Marco Agus et al. "Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience." Briefings in Bioinformatics 24, no. 1 (2023): bbac491. doi:10.1093/bib/bbac491

2022

  • Dong, Taiwei, Min Li, Feng Gao, Peifeng Wei, and Jian Wang. "Construction and imaging of a neurovascular unit model." Neural Regeneration Research 17, no. 8 (2022): 1685. doi:10.4103%2F1673-5374.332131

  • Beyer, Johanna, Jakob Troidl, Saeed Boorboor, Markus Hadwiger, Arie Kaufman, and Hanspeter Pfister. "A Survey of Visualization and Analysis in High‐Resolution Connectomics." In Computer Graphics Forum, vol. 41, no. 3, pp. 573-607. 2022. doi:10.1111/cgf.14574

  • Chindemi, Giuseppe, Marwan Abdellah, Oren Amsalem, Ruth Benavides-Piccione, Vincent Delattre, Michael Doron, András Ecker et al. "A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex." Nature Communications 13, no. 1 (2022): 3038. doi:10.1038/s41467-022-30214-w

  • Huang, Qing, Tingting Cao, Shaoqun Zeng, Anan Li, and Tingwei Quan. "Minimizing Probability Graph Connectivity Cost for Discontinuous Filamentary Structures Tracing in Neuron Image." IEEE Journal of Biomedical and Health Informatics 26, no. 7 (2022): 3092-3103. doi:10.1109/JBHI.2022.3147512

  • Iavarone, Elisabetta, Jane Simko, Ying Shi, Marine Bertschy, María García-Amado, Polina Litvak, Anna-Kristin Kaufmann et al. "Thalamic control of sensory enhancement and sleep spindle properties in a biophysical model of thalamoreticular microcircuitry." bioRxiv (2022): 2022-02. doi:10.1101/2022.02.28.482273

  • Zhu, Xiaoqiang, Xiaomei Liu, Sihu Liu, Yalan Shen, Lihua You, and Yimin Wang. "Robust quasi-uniform surface meshing of neuronal morphology using line skeleton-based progressive convolution approximation." Frontiers in Neuroinformatics 16 (2022). doi:10.3389/fninf.2022.953930

  • Walker, Logan A., Jennifer S. Williams, Ye Li, Douglas H. Roossien, Wei Jie Lee, Nigel S. Michki, and Dawen Cai. "nGauge: Integrated and extensible neuron morphology analysis in Python." Neuroinformatics 20, no. 3 (2022): 755-764. doi:10.1007/s12021-022-09573-8

  • Jiang, Jiaxiang, Michael Goebel, Cezar Borba, William Smith, and B. S. Manjunath. "3D Neuron Morphology Analysis." arXiv preprint arXiv:2212.07044 (2022). doi:10.48550/arXiv.2212.07044

  • Reimann, Michael W., Sirio Bolaños Puchet, Daniela Egas Santander, Jean-Denis Courcol, Alexis Arnaudon, Benoît Coste, Thomas Delemontex et al. "Modeling and Simulation of Rat Non-Barrel Somatosensory Cortex. Part I: Modeling Anatomy." bioRxiv (2022): 2022-08. doi:10.1101/2022.08.11.503144

  • Zehtabian, Amin, Joachim Fuchs, Britta J. Eickholt, and Helge Ewers. "Automated Analysis of Neuronal Morphology through an Unsupervised Classification Model of Neurites." bioRxiv (2022): 2022-03. doi:10.1101/2022.03.01.482454

  • Shen, Yalan, and Jun Fan. "Neurite mesh generation based on pre-processing." In CIBDA 2022; 3rd International Conference on Computer Information and Big Data Applications, pp. 1-4. VDE, 2022. IEEE

  • Shen, Yalan, and Jun Fan. "Mesh generation of neuron cell body." In CIBDA 2022; 3rd International Conference on Computer Information and Big Data Applications, pp. 1-5. VDE, 2022. IEEE

  • Abdellah, Marwan, Juan José García Cantero, Alessandro Foni, Nadir Román Guerrero, Elvis Boci, and Felix Schürmann. "Meshing of Spiny Neuronal Morphologies using Union Operators." (2022). doi:10.2312/cgvc.20221168

  • Bijari, Kayvan. "Enhanced Semi-Automated Metadata Extraction, Acquisition, and Management Via Web Technologies and Machine Learning Models for NeuroMorpho.Org." PhD diss., George Mason University, 2022. Link

  • Lin, Jinwei. "3D Human Movement Pose Generation Based on Pre-trained AI Model with Skeleton Constraint Analysis and Intelligent Prediction." In 2022 IEEE 22nd International Conference on Communication Technology (ICCT), pp. 1582-1589. IEEE, 2022. doi:10.1109/ICCT56141.2022.10072686

2021

  • O'Leary, Liam Anuj, Claudia Belliveau, Maria Antonietta Davoli, Jie Christopher Ma, Arnaud Tanti, Gustavo Turecki, and Naguib Mechawar. "Widespread decrease of cerebral vimentin-immunoreactive astrocytes in depressed suicides." Frontiers in psychiatry 12 (2021): 640963. doi:10.3389/fpsyt.2021.640963

  • Abdellah, Marwan, Alessandro Foni, Eleftherios Zisis, Nadir Roman Guerrero, Samuel Lapere, Jay S. Coggan, Daniel Keller, Henry Markram, and Felix Schürmann. "Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics." Bioinformatics 37, no. Supplement_1 (2021): i426-i433. doi:10.1093/bioinformatics/btab280

  • Bijari, Kayvan, Gema Valera, Hernán López-Schier, and Giorgio A. Ascoli. "Quantitative neuronal morphometry by supervised and unsupervised learning." STAR protocols 2, no. 4 (2021): 100867. doi:10.1016/j.xpro.2021.100867

  • Bingham, Clayton S., Martin Parent, and Cameron C. McIntyre. "Histology-driven model of the macaque motor hyperdirect pathway." Brain Structure and Function 226, no. 7 (2021): 2087-2097. doi:10.1007/s00429-021-02307-7

  • Mousa, Mohamed H., and Sherif M. Elbasiouny. "Estimating the effects of slicing on the electrophysiological properties of spinal motoneurons under normal and disease conditions." Journal of Neurophysiology 125, no. 4 (2021): 1450-1467. doi:10.1152/jn.00543.2020

  • Pastor, Luis, Sofia Bayona, Juan P. Brito, María Cuevas, Isabel Fernaud, Sergio Emilio Galindo, Juan José García-Cantero et al. "A Unified Framework for Neuroscience Morphological Data Visualization." Applied Sciences 11, no. 10 (2021): 4652. doi:10.3390/app11104652

  • Har-Gil, Hagai, Yoav Jacobson, Alvar Prönneke, Jochen F. Staiger, Omri Tomer, Dan Halperin, and Pablo Blinder. "Neural Collision Detection: an open source library to study the three-dimensional interactions of neurons and other tree-like structures." bioRxiv (2021): 2021-07. doi:10.1101/2021.07.20.452894

  • Mousa, Mohamed H., and Sherif M. Elbasiouny. "Cellular and Molecular Properties of Neurons: Estimating the effects of slicing on the electrophysiological properties of spinal motoneurons under normal and disease conditions." Journal of Neurophysiology 125, no. 4 (2021): 1450. doi:10.1152%2Fjn.00543.2020

  • Walter, Florian MJ. "**Advanced Embodied Learning." PhD diss., Technische Universität München, 2021. Link

  • Döring, André, Maryam Afzali, Elena Kleban, Roland Kreis, and Derek K. Jones. "Realistic simulations of diffusion MR spectroscopy: The effect of glial cell swelling on non-Gaussian and anomalous diffusion." Link

2020

  • Huang, Qing, Yijun Chen, Shijie Liu, Cheng Xu, Tingting Cao, Yongchao Xu, Xiaojun Wang et al. "Weakly supervised learning of 3D deep network for neuron reconstruction." Frontiers in Neuroanatomy 14 (2020): 38. doi:10.3389/fnana.2020.00038

  • Ecker, András, Armando Romani, Sára Sáray, Szabolcs Káli, Michele Migliore, Joanne Falck, Sigrun Lange et al. "Data‐driven integration of hippocampal CA1 synaptic physiology in silico." Hippocampus 30, no. 11 (2020): 1129-1145. doi:10.1002/hipo.23220

  • Abdellah, Marwan, Nadir Roman Guerrero, Samuel Lapere, Jay S. Coggan, Daniel Keller, Benoit Coste, Snigdha Dagar, Jean-Denis Courcol, Henry Markram, and Felix Schürmann. "Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis." Bioinformatics 36, no. Supplement_1 (2020): i534-i541. doi:10.1093/bioinformatics/btaa461

  • Boges, Daniya, Marco Agus, Ronell Sicat, Pierre J. Magistretti, Markus Hadwiger, and Corrado Calì. "Virtual reality framework for editing and exploring medial axis representations of nanometric scale neural structures." Computers & Graphics 91 (2020): 12-24. doi:10.1016/j.cag.2020.05.024

  • Velasco, Ivan, Pablo Toharia, Ruth Benavides-Piccione, Isabel Fernaud-Espinosa, Juan P. Brito, Susana Mata, Javier DeFelipe, Luis Pastor, and Sofia Bayona. "Neuronize v2: bridging the gap between existing proprietary tools to optimize neuroscientific workflows." Frontiers in Neuroanatomy 14 (2020): 585793. doi:10.3389/fnana.2020.585793

  • Amsalem, Oren, James King, Michael Reimann, Srikanth Ramaswamy, Eilif Muller, Henry Markram, Israel Nelken, and Idan Segev. "Dense computer replica of cortical microcircuits unravels cellular underpinnings of auditory surprise response." BioRxiv (2020): 2020-05. doi:10.1101/2020.05.31.126466

  • Grein, Stephan Matthias. "A Novel Mesh Generator for the Numerical Simulation of Multi-Scale Physics in Neurons." Temple University, 2020. Link

2019

  • Iyengar, Raghu Sesha, Madhav Vinodh Pithapuram, Avinash Kumar Singh, and Mohan Raghavan. "Curated model development using NEUROiD: A web-based NEUROmotor integration and design platform." Frontiers in Neuroinformatics 13 (2019): 56. doi:10.3389/fninf.2019.00056

  • Fulmer, Willis, Tahir Mahmood, Zhongyu Li, Shaoting Zhang, Jian Huang, and Aidong Lu. "ImWeb: Cross-platform immersive web browsing for online 3D neuron database exploration." In Proceedings of the 24th International Conference on Intelligent User Interfaces, pp. 367-378. 2019. doi:10.1145/3301275.3302319

  • Cinelli, Ilaria, Michel Destrade, Peter McHugh, Antonia Trotta, Michael Gilchrist, and Maeve Duffy. "Head-to-nerve analysis of electromechanical impairments of diffuse axonal injury." Biomechanics and Modeling in Mechanobiology 18, no. 2 (2019): 361-374. doi:10.1007/s10237-018-1086-8

  • Karlsson, Jonas, Marwan Abdellah, Sebastien Speierer, Alessandro Foni, Samuel Lapere, and Felix Schürmann. "High fidelity visualization of large scale digitally reconstructed brain circuitry with signed distance functions." In 2019 Ieee Visualization Conference (Vis), pp. 176-180. IEEE, 2019. doi:10.1109/VISUAL.2019.8933693

  • Boges, Daniya, Corrado Calì, Pierre J. Magistretti, Markus Hadwiger, Ronell Barrera Sicat, and Marco Agus. "Immersive environment for creating, proofreading, and exploring skeletons of nanometric scale neural structures." (2019). doi:10.2312/stag.20191360

  • Zhong, Zhicheng, and Hongqin Li. "Analysis and Simulation of Morphology Algorithm for Fiber Optic Hydrophone Array in Marine Seismic Exploration." Journal of Coastal Research 94, no. SI (2019): 145-148. doi:10.2112/SI94-029.1

  • Little, Spencer, and Kathryn Davidson. "Capstone Proposal." (2019).

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